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PubMed2006

Optimizing selection on multiple identified quantitative trait loci in population with overlapping generations.

A method was developed to model and optimize selection on multiple identified quantitative trait loci (QTLs) and polygenic estimated breeding value, in order to maximize a weighted sum of cumulative response to selection over multiple years in a population with overlapping generations. The model allows for a population with multiple sex-age classes, different number of age class between sires and dams, and varied genetic contribution of the age class. The optimization problem was formulated as a multiple-stage optimal control problem and solved by a forward and backward iteration loop. The practical utility of this method was illustrated in an example of pig breeding population with overlapping generations. The selection response of this method was compared with standard QTL selection and conventional best linear unbiased prediction (BLUP) selection. Simulation results show that optimal selection achieved greater selection response than either standard QTL or conventional BLUP selections. The influence of population structure on optimal selection was significant. Optimal QTL selection and standard QTL selection were more favorable in a population with overlapping generations than discrete generations, and obtained more benefits relative to conventional BLUP selection in a population with overlapping generations. Optimal QTL selection relative to conventional BLUP selection is also more favorable following increase of genetic contribution of two-year-old boars and sows in a population with overlapping generations.

Algorithms↗

PubMed1997

Genetic evaluation of dairy cattle using test day yields and random regression model.

A model for analyzing test day records that contains both fixed and random regression coefficients was applied to the genetic evaluation of first lactation data for Canadian Holstein dairy cows. Data were 5.1 million test day records with milk, fat, and protein yields from calvings between 1988 and 1995 from herds in four regions of Canada. Each evaluated animal received five predictions for each trait representing the random regression coefficients. From these solutions, a range of estimated breeding values for various parts of the lactation could be calculated. Three genetic measures of persistency were compared. Bulls could be selected for both yields and persistency of their daughters in whatever combination was desirable. Test day analyses could result in monthly genetic evaluations for yield traits.

Analysis of Variance↗

PubMed1988

Mitochondrial respiratory metabolism and performance of cattle.

Two groups of cows were sampled to study variation of mitochondrial metabolism. The first group included 10 lactating and five gestating Holstein cows, representing available phenotypic extremes for milk yield. The second group included 13 Angus, 13 Brangus and 13 Hereford cows, representing available extremes within breeds for growth breeding value ratios. Consistently poor mitochondrial samples were obtained from gestating cows; these were excluded from analyses. Linear correlations of Holstein mitochondrial respiratory activities with sire-predicted difference for milk and milk fat ranged from -.35 to .15. Correlations of dam and cow indices and cow yields for milk with acceptor-stimulated mitochondrial respiration, oxidative phosphorylation efficiency (adenosine diphosphate:oxygen ratio [ADP:O ratio]) and adenosine triphosphate (ATP) synthesis rate were .25 to .48, consistently higher than for milk fat, -.06 to .17. No differences among beef breeds in mitochondrial respiration rates, coupling of respiration to phosphorylation, ADP:O ratio or ATP synthesis rate were detected by repeated measures analyses of variance. No patterns were evident among correlations of the mitochondrial characteristics and growth and milk traits in beef cattle. These initial findings indicate that variability in the mitochondrial respiratory activities measured has less relation to weaning and yearling growth traits of beef cattle than to milk yield of Holstein cattle.

Animals↗

PubMed2005

Scrapie resistance alleles are not associated with lower prolificity in Rasa Aragonesa sheep.

Scrapie is a prion disease characterised by the accumulation of the pathological associated form of cellular prion protein (PrP(SC)) in the central nervous system. Susceptibility to scrapie is associated with polymorphism in the ovine prion protein (PrP) gene. The European Union has implemented scrapie control programs, relying on selective breeding for scrapie resistance; the use of ARR-carrier and the exclusion of VRQ-carrier were recommended. In this study, 4323 individuals from Rasa Aragonesa Sheep breed were genotyped for the PrP gene and the individual estimated breeding values (EBV) for prolificity were calculated. Most represented PrP alleles do not work against prolificity. Only a significant association between VRQ/VRQ genotype and a lower EBV was observed (p = 0.027, eta2 = 0.002). Therefore, avoiding reproduction of VRQ/VRQ individuals would not cause negative effect regarding prolificity.

Alleles↗

PubMed1986

Within-herd phenotypic, genetic and environmental trend lines for beef cattle breeders.

Computational procedures were developed to compute within-herd phenotypic, genetic and environmental trend lines on a breed-wide basis by using best linear unbiased estimates of fixed effects and predictors of random sire and dam genetic effects. Procedures were demonstrated by using weaning weight performance records from 20 herds participating in the American Angus Herd Improvement Program. Current evaluation procedures used by several beef breed associations make it possible to provide such information to breeders on a routine basis, along with within-herd breeding values. The within-herd genetic trends are relative to the national genetic evaluation base. Procedures are summarized in addition to presentation of within-herd trend lines for four of the 20 herds, demonstrating the utility of such information to breeders, along with a discussion of several alternative presentation formats.

Animal Husbandry↗

PubMed1991

National genetic improvement programs for dairy cattle in the United States.

Rate of genetic improvement for milk yield has been increasing in recent years. Cows born in 1986 were about 135 kg superior in breeding value for milk yield to those born in 1985. Over 2.2 million cows contribute new data to genetic evaluations for production traits annually. These evaluations are computed with an animal model that provides best linear unbiased predictions of transmitting abilities for milk, fat, and protein yields and fat and protein percentages. The model includes effects of management group, permanent environment, herd-sire interaction, and animal genetic merit. Unknown-parent groups represent the genetic merit of base populations defined by birth year and sex. Type appraisal data are collected by breed associations and are evaluated with a sire model. Holstein cow evaluations are computed using scores from all appraisals and a multitrait model; evaluations for other breeds are computed using all appraisal scores, a repeatability model, and a single-trait system. Dystocia data are collected by individual AI organizations and dairy records processing centers; they are analyzed by a categorical-trait sire model at Iowa State University with support from the National Association of Animal Breeders. The AI organizations have been extremely important in increasing rate of genetic progress by increasing numbers of young bulls sampled, increasing selection intensity of bull dams through multiple ovulation and embryo transfer, and shortening generation interval through the use of younger cows and some virgin heifers as bull dams. (ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1982

Genetic and environmental trends of milk production in a closed flock of Beetal goats.

Genetic and environmental trends in first lactation milk yield, first lactation length, milk yield per day of lactation, and milk yield per day of kidding interval were determined from records on 1101 nannies, progeny of 86 sires, and spread over 37 yr. Genetic progress was computed from the regression of production on time with adjustment for deviation from random mating according to age, breeding value of dam, culling, and maternal effects. Genetic trends were positive for milk yield and yield per day of lactation and were 1.05 and 1.02% of their respective flock averages. Genetic trends were negative for lactation length and yield per day of kidding interval and were 1.19 and .43% of their respective flock means.

Animals↗

PubMed2004

An association study using AFLP markers and application to a beef cattle breeding population.

Using amplified fragment length polymorphism (AFLP) fingerprinting, selective genotyping was performed to determine if this method was effective for selecting superior breeding stock. Forty-eight cows with extreme genetic merit for beef marbling score (BMS) were selected from a population of Japanese Black cattle (n = 4462), including 25 with the highest for predicted breeding value (PBV) and 23 with the lowest. Sixteen AFLP fragments were selected for further analysis based on fragment frequency differences between the high and low groups. A linear discriminant analysis using these AFLP fragments was applied in order to derive a discriminant function that classified the cows into high and low groups. Seven of the 16 fragments were included in the resulting function and the discriminant scores (general genetic values, GGV) of the 48 cows were calculated using the function. These cows were clearly separated into high and low groups by GGV with a correlation ratio of 0.91 (discriminative error of 2.1%). The same function was then applied to 121 additional cows that were randomly selected from the original population. A significant regression coefficient of GGV on BMS-PBV (R2 = 0.45) was obtained, which indicates that the GGV can be used as a selection criterion for BMS in this population. These results suggest that AFLP fingerprinting can be used for animal breeding without identifying the underlying genes affecting the trait of interest.

Agriculture↗

PubMed2002

Genetic evaluation of bulls and cows with single- and multiple-country test-day models.

First-lactation milk yield test-day records on cows from Australia, Canada, Italy, and New Zealand were analyzed by single- and multiple-country random regression models. Models included fixed effects of herd-test day and breed composition-age at calving-season of calving by days in milk, and random regressions with Legendre polynomials of order four for animal genetic and permanent environmental effects. Milk yields in different countries were defined as genetically different traits for the purpose of multiple-trait model. Estimated breeding values of bulls and cows from single- and multiple-trait models were compared within and across countries for two traits: total milk yield in lactation and lactation persistency, defined as the linear coefficient of animal genetic curve. Correlations between single- and multiple-trait evaluations within country for total yield were higher than 0.95 for bulls and close to 1 for cows. Correlations for lactation persistency were lower than respective correlations for total yield. Between country correlations for lactation yield ranged from 0.93 to 0.96, indicating different ranking of bulls on different country scales under multiple-trait model. Lactation persistency had in general lower between-country correlations, with the highest values for Canada-Italy and Australia-New Zealand pairs, for both single- and multiple-country models. Although multiple-country random regression test-day model was computationally feasible for four countries, the same would not be true for routine international genetic evaluation in the near future.

Age Factors↗

PubMed2002

Strategies for continual application of marker-assisted selection in an open nucleus population.

The objectives of this study were to develop and simulate the implementation of several strategies for repeated application of quantitative trait loci (QTL) detection and marker-assisted selection (MAS) and to compare the short-term and continual genetic responses. A finite locus model was simulated with 20 QTL randomly distributed across 30 chromosome. Three hundred markers were evenly spaced across the genome. Allelic effects were sampled from a double exponential distribution. A daughter design was used every generation to determine the marker alleles favorably associated to QTL alleles. The MAS was applied within family to young bulls, before progeny testing, as part of an open nucleus. Young bulls were selected using strategies based on 1) the single marker with greatest contrast (BEST1), 2) the sum of n greatest contrasts (BESTn), 3) the best n contrasts, limited to one per chromosome (LIMn), 4) the sum of all contrasts exceeding a given threshold n (THRESn), and 5) the sum of contrasts exceeding a threshold, but limited to one per chromosome (LIMT). The maximum progress was achieved by strategies that selected upon several markers flanking multiple QTL in each generation. When THRES was applied, the mean true breeding value (TBV) of selected bulls was increased by 11.98% (over conventional selection) versus 6.73% for BEST1 in the first generation. Applying a full genome scan in each generation allowed selection for different QTL across time. By selecting for multiple QTL over time, MAS maintained superiority over conventional selection for many generations.

Alleles↗

PubMed2007

Genetic analysis of postpartum measures of luteal activity in dairy cows.

The objective of this study was to estimate genetic parameters for measures of luteal activity during the first 60 d postpartum. Analyses were made with different sampling intervals to investigate the possibility of combining progesterone measurement with routinely performed milk recording. Progesterone level in milk as an indicator of female fertility when selecting sires in a progeny-testing scheme was also examined. Data were collected from 1996 to 1999, and comprised 1,212 lactations from 1,080 British Holstein-Friesian cows at 8 commercial dairy farms in the United Kingdom. Milk samples for progesterone analysis were collected thrice weekly. Mixed linear animal models were used to analyze the data. Heritability for the percentage of samples with luteal activity during the first 60 d postpartum (PLA) was 0.30 and decreased with more infrequent sampling to 0.25, 0.20, and 0.14 for weekly, twice-monthly, and monthly sampling, respectively. Measures of PLA had a high negative genetic correlation with prolonged anovulation (-0.53 for monthly sampling, < -0.87 otherwise) and a moderate positive genetic correlation with persistent corpus luteum in the first estrus cycle (>0.65 if at least twice-monthly sampling). Genetic correlations with interval from calving to commencement of luteal activity were close to -1 for all PLA measurements and the selection index calculations showed that monthly progesterone sampling could be used with high accuracy (0.80 with 50 daughters per bull) to predict breeding values for commencement of luteal activity. Progesterone analysis at the time of regular milk recording could thereby be used to select for an early interval from calving to commencement of luteal activity and, at the same time, a decreased frequency of prolonged anovulation during the postpartum period.

Animals↗

PubMed2006

The use of a random regression model to account for change in racing speed of German trotters with increasing age.

In a genetic analysis of German trotters, the performance trait racing time per km was analysed by using a random regression model on six different age classes (2-, 3-, 4-, 5- and 6-year-old and older trotters; the age class of 3-year-old trotters was additionally divided by birth months of horses into two seasons). The best-fitting random regression model for the trait racing time per km on six age classes included as fixed effects sex, race track, condition of race track (fitted as second-order polynomial on age), distance of race and each driver (fitted as first-order polynomial on age) as well as the year-season (fitted independent of age). The random additive genetic and permanent environmental effects were fitted as second-order polynomials on age. Data consisted of 138,620 performance observations from 2,373 trotters and the pedigree data contained 9,952 horses from a four-generation pedigree. Heritabilities for racing time per km increased from 0.01 to 0.18 at age classes from 2- to 4-year-old trotters, then slightly decreased for 5 year and substantially decreased for 6-year-old horses. Genetic correlations of racing time per km among the six age classes were very high (rg = 0.82-0.99). Heritability was h2 = 0.13 when using a repeatability animal model for racing time per km considering the six age classes as fixed effect. Breeding values using repeatability analysis over all and within age classes resulted in slightly different ranking of trotters than those using random regression analysis. When using random regression analysis almost no reranking of trotters over time took place. Generally, the analyses showed that using a random regression model improved the accuracy of selection of trotters over age classes.

Aging↗

PubMed2005

The metabolic cost of egg production is repeatable.

The metabolic cost of egg production in birds (passerines) has been measured as a 16-27% increase in basal or resting metabolic rate (BMR and RMR, respectively) when comparing non-breeding values with those in egg-producing individuals. However, available data to date have been obtained in free-living birds and may thus be confounded by the effect of variable ecological conditions on non-reproductive physiological machinery (organ mass or metabolic activity) which might contribute to measured variation in RMR. Here, we show that in captive, controlled conditions, the process of egg formation induces a 22% increase in RMR in female zebra finches Taeniopygia guttata. Among individuals, variation in laying RMR is independent of egg mass, clutch size or total clutch mass. Importantly, we show that individual variation in both non-breeding and laying RMR is repeatable over periods of at least 8-10 months, i.e. individual variation in RMR remained constant over time for any given physiological state. This suggests that the metabolic cost of egg formation should respond to selection. However, we also show that in males, but not females, repeatability of RMR declines over time even when birds are kept in constant controlled conditions.

Analysis of Variance↗

PubMed2003

Genetic parameters for body condition score and its relationship with type and production traits in Swiss Holsteins.

The objectives of this study were to estimate the genetic and environmental parameters between body condition score (BCS) and 27 conformation and 3 production traits in Swiss Holstein cattle. The dataset consisted of 31,500 first-lactation cows, which were daughters of 545 sires in 1867 herds. Bivariate sire models with relationships among sires were used to estimate parameters. Least squares means for BCS by lactation stage show that cows lose BCS up to 5 mo after calving and gain BCS prior to the next calving. Regression models showed that an increase in age and percentage of Holstein genes results in an increase and decrease in BCS, respectively. Heritability (h2) was 0.24 for BCS score, which indicates good potential for selection. Sire estimated breeding values for BCS ranged from -0.46 to +0.51 units. Heritabilities ranged from 0.08 (heel depth) to 0.46 (rump width) for type traits and 0.23 to 0.29 for yield traits. Genetic correlations of BCS with 8 conformation traits were significant; stature (0.28), heart girth (0.21), strength (0.17), loin (-0.39), body capacity (0.19), dairy character (-0.35), udder quality (-0.42), and teat position rear (-0.33). Milk production and body condition have an unfavorable genetic correlation (-0.12 to -0.17). These results show that selection for good body condition, body conformation, and optimal milk production is possible and their genetic associations reported here will be useful for designing Swiss breeding goals.

Analysis of Variance↗

PubMedDate not supplied

[The genotypic evaluation of bulls for the milk productivity of their daughters].

Breeding value of stud bulls was evaluated by methods of comparison of daughter and herd-mate productivity for milk production at the reproductive crossing of Red Step and Holstein cattle. It was shown with a sufficient degree of certainty and legitimacy that such methods of comparison of Holstein bull daughters with the cross-bred herd mates without regard to their inheritance may be extensively used.

Animals↗

PubMed1999

Comparison of milk production of the progeny of BLAD-carrier and healthy Holstein bulls in Hungary.

'Bovine Leukocyte Adhesion Deficiency' (BLAD) is a recessive monofactorial, lethal inheritable defect occurring in Holstein-Friesian cattle and often passed on by well-known top bulls. The aim of this study was to find a relationship between the BLAD genotype of bulls, their genetic evaluation for milk and their daughters' milk production. BLAD-carrier and healthy bulls were compared on the basis of their breeding value published in November 1997. The first 100 bulls ranked according to the Total Production Index (TPI) were used, including nine BLAD carriers with 2,835 daughters and 77 healthy sires with 21,950 female progenies. For 14 bulls the BLAD genotype was not indicated. The healthy animals significantly outperformed the BLAD carriers, which result contradicts our earlier findings (Dohy et al., 1996; Jánosa and Dohy, 1997). In a BLAD elimination programme, the identification of BLAD carriers and properly planned mating are of great importance in order to avoid 'inter se' mating of BLAD-carrier top animals which can be of significant influence in Holstein breeding.

Alleles↗

PubMed2001

Genetic evaluation of carcass traits in Simmental-sired cattle at different slaughter end points.

Our objectives were to estimate genetic parameters for carcass traits and evaluate the influence of slaughter end point on estimated breeding values (BV). Data provided by the American Simmental Association were divided into three sets: 1) 9,604 records of hot carcass weight (CW) and percentage retail cuts (PRC), 2) 6,429 records of CW, PRC, and marbling score (MS), and 3) 1,780 records of CW, PRC, MS, fat thickness (FT), and longissimus muscle area (LMA). Weaning weights (WW) from animals with carcass data and from their weaning contemporaries were used. Data were analyzed with a multiple-trait animal model and REML procedures to estimate genetic parameters and BV on an age-, CW-, MS-, or FT-constant basis. The model for carcass traits included fixed contemporary group and covariates for breed, heterozygosity, and slaughter end point and random additive direct genetic and residual effects. Weaning weight was preadjusted for founder effects, direct and maternal heterosis, age of dam, and age of calf. The model for WW included fixed contemporary group and random additive direct genetic, maternal genetic, maternal permanent environment, and residual effects. Heritabilities from data set 1 were 0.34 for CW and 0.25 for PRC on an age-constant basis and 0.25 for PRC on a CW end point. Heritabilities for data set 2 were 0.35, 0.24, and 0.36 for CW, PRC, and MS, respectively, on an age-constant basis. Data set 2 heritabilities were 0.25 for PRC and 0.34 for MS on a CW-constant basis and 0.33 for CW and 0.25 for PRC at a constant MS end point. Heritabilities on an age-constant basis for data set 3 were as follows: CW, 0.32; PRC, 0.09; MS, 0.12; FT, 0.10; and LMA, 0.26. Heritability estimates for data set 3 on a CW-, MS-, and FT-constant basis were similar to those on an age-constant basis. Heritabilities were 0.12 for PRC, 0.12 for MS, 0.14 for FT, and 0.22 for LMA on a CW-constant basis; 0.30 for CW, 0.09 for PRC, 0.10 for FT, and 0.28 for LMA at a constant MS end point; and 0.33, 0.17, 0.13, and 0.29 for CW, PRC, MS, LMA on a FT-constant basis. Genetic correlations among traits varied across groups and end points but suggested that it should be possible to select for improved lean yield without sacrificing quality grade. Correlations were calculated among BV computed at different end points. Adjustment to various end points resulted in some changes in BV and reranking of sires, especially for PRC; however, the number of records available had a larger influence than slaughter end point.

Animals↗

PubMed2006

Wrong and missing sire information affects genetic gain in the Angeln dairy cattle population.

In the present study, molecular genetic markers were used to help estimate the degree of wrong sire information in the German Angeln dairy cattle population. Sixteen polymorphic microsatellite markers were genotyped on 5 different paternal half-sib families with a total of 805 daughters. For the genotyping process, blood samples of the daughters and semen samples of the sires were used. Allelic frequencies and exclusion probabilities were estimated. The simultaneous effect of wrong (WSI) and missing sire information (MSI) on the reliability of estimated breeding values and on the genetic gain was investigated using deterministic simulations. For these simulations, different values for the number of daughters per sire, heritability, WSI, and MSI were chosen. The estimated proportion of the WSI was 7% in the German Angeln dairy cattle population. The combined impact of WSI and MSI on the genetic gain was relatively large, especially in the case of small progeny size per sire and low heritability. The impact of WSI was more harmful than MSI on response to selection.

Alleles↗